Your browser doesn't support javascript.
loading
Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.
Suchan, Tomasz; Espíndola, Anahí; Rutschmann, Sereina; Emerson, Brent C; Gori, Kevin; Dessimoz, Christophe; Arrigo, Nils; Ronikier, Michal; Alvarez, Nadir.
Afiliação
  • Suchan T; Department of Ecology and Evolution, University of Lausanne, Switzerland; W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland. Electronic address: t.suchan@botany.pl.
  • Espíndola A; Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
  • Rutschmann S; Department of Ecology and Evolution, University of Lausanne, Switzerland; Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain.
  • Emerson BC; Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain; School of Biological Sciences, University of East Anglia, Norwich, UK.
  • Gori K; Department of Veterinary Medicine, University of Cambridge, UK.
  • Dessimoz C; Department of Ecology and Evolution, University of Lausanne, Switzerland; Department of Veterinary Medicine, University of Cambridge, UK; Center for Integrative Genomics, University of Lausanne, Switzerland; Department of Genetics, Evolution & Environment and Department of Computer Science, Univ
  • Arrigo N; Department of Ecology and Evolution, University of Lausanne, Switzerland.
  • Ronikier M; W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland.
  • Alvarez N; Department of Ecology and Evolution, University of Lausanne, Switzerland. Electronic address: nadir.alvarez@unil.ch.
Mol Phylogenet Evol ; 114: 189-198, 2017 09.
Article em En | MEDLINE | ID: mdl-28645767
ABSTRACT
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years. Here we examine the potential and limitations of one of such techniques-Restriction-site Associated DNA (RAD) sequencing, a method that produces thousands of (mostly) anonymous nuclear markers, in disentangling the phylogeny of the fly genus Chiastocheta (Diptera Anthomyiidae). In Europe, this genus encompasses seven species of seed predators, which have been widely studied in the context of their ecological and evolutionary interactions with the plant Trollius europaeus (Ranunculaceae). So far, phylogenetic analyses using mitochondrial markers failed to resolve monophyly of most of the species from this recently diversified genus, suggesting that their taxonomy may need a revision. However, relying on a single, non-recombining marker and ignoring potential incongruences between mitochondrial and nuclear loci may provide an incomplete account of the lineage history. In this study, we applied both classical Sanger sequencing of three mtDNA regions and RAD-sequencing, for reconstructing the phylogeny of the genus. Contrasting with results based on mitochondrial markers, RAD-sequencing analyses retrieved the monophyly of all seven species, in agreement with the morphological species assignment. We found robust nuclear-based species assignment of individual samples, and low levels of estimated contemporary gene flow among them. However, despite recovering species' monophyly, interspecific relationships varied depending on the set of RAD loci considered, producing contradictory topologies. Moreover, coalescence-based phylogenetic analyses revealed low supports for most of the interspecific relationships. Our results indicate that despite the higher performance of RAD-sequencing in terms of species trees resolution compared to cytoplasmic markers, reconstructing inter-specific relationships among recently-diverged lineages may lie beyond the possibilities offered by large sets of RAD-sequencing markers in cases of strong gene tree incongruence.
Assuntos
Palavras-chave

Texto completo: 1 Base de dados: MEDLINE Assunto principal: DNA / Dípteros Idioma: En Ano de publicação: 2017 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: DNA / Dípteros Idioma: En Ano de publicação: 2017 Tipo de documento: Article